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Crystal structure of mouse thiamine triphosphatase in complex with thiamine diphosphate, orthophosphate and magnesium ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A64 PDB ENTRY 5A64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 27 % PEG 3350,0.2M NACL, 0.1 M TRIS PH 9.0, 0.2M MGCL2
Crystal Properties Matthews coefficient Solvent content 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.483 α = 90 b = 105.483 β = 90 c = 111.805 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2015-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.98 49.4 99.7 0.11 19.66 25.6 44247 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.1 98.6 1.5 1.9 23.85
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5A64 1.98 49.39 42091 2155 99.72 0.21027 0.20784 0.2341 0.25818 0.2687 RANDOM 51.63
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.89 1.89 -3.78
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.711 r_dihedral_angle_2_deg 34.35 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 13.893 r_sphericity_bonded 8.912 r_dihedral_angle_1_deg 5.49 r_mcangle_it 3.352 r_scbond_it 3.051 r_mcbond_it 2.722 r_mcbond_other 2.722
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 37.711 r_dihedral_angle_2_deg 34.35 r_dihedral_angle_4_deg 16.711 r_dihedral_angle_3_deg 13.893 r_sphericity_bonded 8.912 r_dihedral_angle_1_deg 5.49 r_mcangle_it 3.352 r_scbond_it 3.051 r_mcbond_it 2.722 r_mcbond_other 2.722 r_rigid_bond_restr 1.708 r_angle_refined_deg 1.515 r_angle_other_deg 0.933 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3089 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing